RNase E Regulation
Overview RNase E is an endoribonuclease that controls rRNA maturation and mRNA decay (2). The main function of RNase lies in the processing of ribosomal RNA molecules and tRNA molecules. RNase E also degrades its own mRNA by cleaving it within the 5'-UTR, which in turn controls its own gene expression (2). Substrates for RNase E cleavage generally are single-stranded, and have a monophosphate on their 5' end. Most mRNA's have a triphosphate at their 5' end. The phosphohydrolase RppH cleaves the 5' pyrophosphate, leaving a monophosphate which targets the substrate for degradation (3). This regulation system is most notably studied in E. coli. '' RNase E RNase E is an endoribonuclease, which means that it cleaves a phosphodiester bond within a polynucleotide chain. RNase degrades mRNA by cutting the strand near the 5' untranslated region. The newly cut strand then undergoes another round of cleavage, which makes it shorter (4). The proteolytic cleavage continues until the strand is degraded and able to be used by the cell for bulk nucleotides. RNase E requires either Mn or Mg a cofactor to function. When these cofactors are absent, the enzyme breaks down into 2 inactive domains (4). RNase E chooses it's substrate based on phosphorylation. It has a high affinity for single-stranded monophosphorylated mRNA strands. RNase E has a 5' sensor that scans an mRNA strand to detect whether the strand is monophosphorylated or triphosphorylated. Additionally, RNase E prefers strands that have a purine in the second position. RppH RppH is a 5' RNA Pyrophosphohydrolase that belongs to the nudix family (1).The Nudix family of phosphohydrolases break phosphate bonds in a substrate. This specific enzyme removes a pyrophosphate from the 5' end of mRNA. This cleavage leaves a monophosphate, which is an ideal substrate for RNase E degradation. RppH and RNase E work in sync with each other. When RppH was deleted from cells, the half-life of most mRNA's was doubled (1), which means that they were not getting degraded. The mRNA was not getting degraded due to the triphosphate on the 5' end, so RNase E was unable to cleave. RNA Degradosome RNase E is the primary component within the multi-protein complex known as the degradosome. The other components are an Enolase, RNA helicase B and polynucleotide phosphorylase (7). RNA helicase B hydrolyzes ATP and uses the energy to unwind RNA. Unwinding of the RNA is the first step in the degradation process. Polynucleotide phosphorylase is an enzyme that has 3' to 5' exoribonuclease activity. this enzyme degrades mRNA transcripts from the 3' end to the 5' end (6). The main function of the degradosome is to degrade mRNA and process ribosomal RNA. Enolase is a glycolytic enzyme that catalyzes the 9th step in breakdown of glucose. In the degradosome, however, the role of the enolase component is not well understood (8). While there are other components to this complex, RNase E has the most catalytic activity and is the only domain out of the fourthat has major catalytic effects on its own. Regulation Interestingly, RNase E autoregulates its own synthesis along with the synthesis of other mRNA transcripts. RNase E is the gene product of the gene ''rne. Rne gene expression is regulated via an autofeedback loop, which means when there is too much of the mRNA transcript it will be degraded by the gene product that it produces. In order to test for this autoregulation, Jain et al fused a lacZ reporter to the first 181 codons of the rne ''gene (4). This gene was then overexpressed and the B-gal levels from the lacZ reporter were examined. The results were very straightforward; as RNase E levels increased the B-gal levels decreased, which means lower ''rne ''gene expression. And vice-versa, as RNase E levels decreased, the B-gal levels increased, which meant higher ''rne ''gene expression (4). RNase E, in addition to its autoregulation, has been shown to regulate other types of RNA molecules; such as ribosomal (rRNA) and transfer RNA (tRNA) (5). The processing of these molecules, however, do not directly correlate with gene expression so they are not relevant to this article. References 1. RppH. '' NEB 2. RNase E: at the interface of bacterial RNA processing and decay. ''Nature 3. Ribonuclease E. Uniprot 4. RNase E autoregulates its synthesis by controlling the degradation rate of its own mRNA in Escherichia coli: unusual sensitivity of the rne transcript to RNase E activity. ''Genes and Development 5. ''RNase E is involved in 5'-end 23S rRNA processing in alpha-Proteobacteria. ''PMID: 12470646 6. ''RNA Components of ''Escherichia coli: ''Evidence for RNA decay. ''PNAS 7. ''Degradosome. ''Wikipedia 8. ''Enolase in the RNA degradosome plays a crucial role in the rapid decay of the glucose transporter mRNA in the response to phosphosugar stress in ''Escherichia coli. PMID: 15522087 IMAGE 1 IMAGE 2